NC_000010.10:g.(?_89711865)_(89712026_?)dup AND PTEN hamartoma tumor syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 4, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001379252.5

Allele description

NC_000010.10:g.(?_89711865)_(89712026_?)dup

Gene:: PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
Variant type:: Duplication
Cytogenetic location:: 10q23.31
Genomic location:: Chr10: 89711865 - 89712026 (on Assembly GRCh37)
Preferred name:: NC_000010.10:g.(?_89711865)_(89712026_?)dup
HGVS:: NC_000010.10:g.(?_89711865)_(89712026_?)dup
This HGVS expression did not pass validation

Condition(s)

Name:: PTEN hamartoma tumor syndrome (PHTS)
Synonyms:: PTEN Hamartomatous Tumour Syndrome
Identifiers:: MONDO: MONDO:0017623; MeSH: D006223; MedGen: C1959582

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001577014	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Aug 4, 2021)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 25640679, 9467011, 21194675, 25669429, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001577014

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Aug 4, 2021)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints.

Newman S, Hermetz KE, Weckselblatt B, Rudd MK.

Am J Hum Genet. 2015 Feb 5;96(2):208-20. doi: 10.1016/j.ajhg.2014.12.017. Epub 2015 Jan 29.

PubMed [citation]

PMID:: 25640679
PMCID:: PMC4320257

Mutation spectrum and genotype-phenotype analyses in Cowden disease and Bannayan-Zonana syndrome, two hamartoma syndromes with germline PTEN mutation.

Marsh DJ, Coulon V, Lunetta KL, Rocca-Serra P, Dahia PL, Zheng Z, Liaw D, Caron S, Duboué B, Lin AY, Richardson AL, Bonnetblanc JM, Bressieux JM, Cabarrot-Moreau A, Chompret A, Demange L, Eeles RA, Yahanda AM, Fearon ER, Fricker JP, Gorlin RJ, Hodgson SV, et al.

Hum Mol Genet. 1998 Mar;7(3):507-15.

PubMed [citation]

PMID:: 9467011

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001577014.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This variant results in a copy number gain of the genomic region encompassing exon(s) 6 of the PTEN gene. While the exact position of this variant cannot be determined from the data, sub-genic copy number gains are generally in tandem (PMID: 25640679). This variant is predicted to be out-of-frame, and may result in an absent or disrupted protein product. Loss-of-function variants in PTEN are known to be pathogenic (PMID: 9467011, 21194675). A similar copy number variant has been observed in individual(s) with clinical features of Cowden syndrome (PMID: 25669429). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 13, 2023

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